GENESIS-package: GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness

Description

The GENESIS package provides methodology for estimating, inferring, and accounting for population and pedigree structure in genetic analyses. The current implementation performs PC-AiR (Conomos et al., 2015, Gen Epi) and PC-Relate (Conomos et al., 2016, AJHG). PC-AiR performs a Principal Components Analysis on genome-wide SNP data for the detection of population structure in a sample that may contain known or cryptic relatedness. Unlike standard PCA, PC-AiR accounts for relatedness in the sample to provide accurate ancestry inference that is not confounded by family structure. PC-Relate uses ancestry representative principal components to adjust for population structure/ancestry and accurately estimate measures of recent genetic relatedness such as kinship coefficients, IBD sharing probabilities, and inbreeding coefficients. Additionally, functions are provided to perform efficient variance component estimation and mixed model association testing for both quantitative and binary phenotypes.

Arguments

Details

Package:

GENESIS

Type:

Package

Version:

2.1.7

Date:

2016-4-1

License:

GPL-3

Depends:

GWASTools

Suggests:

gdsfmt, SNPRelate, RUnit, BiocGenerics, knitr

VignetteBuilder:

knitr

biocViews:

SNP, GeneticVariability, Genetics, StatisticalMethod, DimensionReduction, PrincipalComponent, GenomeWideAssociation, QualityControl, BiocViews

The PC-AiR analysis is performed using the pcair function, which takes genotype data and pairwise measures of kinship and ancestry divergence as input and returns PC-AiR PCs as the ouput. The function pcairPartition is called within pcair and uses the PC-AiR algorithm to partition the sample into an ancestry representative `unrelated subset' and `related subset'. The function plot.pcair can be used to plot pairs of PCs from a class `pcair' object returned by the function pcair. The function king2mat can be used to convert output text files from the KING software (Manichaikul et al., 2010) into an R matrix of pairwise kinship coefficient estimates in a format that can be used by the functions pcair and pcairPartition. The PC-Relate analysis is performed using the pcrelate function, which takes genotype data and PCs from PC-AiR and returns estimates of kinship coefficients, IBD sharing probabilities, and inbreeding coefficients. The functions pcrelateReadKinship, pcrelateReadInbreed, and pcrelateMakeGRM provide utilities for reading and making tables or matrices of the PC-Relate output. There are two functions required to perform SNP genotype association testing with mixed models. First, fitNullMM is called to fit the null model (i.e. no SNP genotype term) including fixed effects covariates, such as PC-AiR PCs, and random effects specified by their covariance structures, such as a kinship matrix created from PC-Relate output using pcrelateMakeGRM. The function fitNullMM uses AIREML to estimate variance components for the random effects, and the function varCompCI can be used to find confidence intervals on the estimates as well as the proportion of total variability they explain; this allows for heritability estimation. Second, assocTestMM is called with the null model output and the genotype data to perform either Wald or score based association tests.

References

Conomos M.P., Reiner A.P., Weir B.S., & Thornton T.A. (2016). Model-free Estimation of Recent Genetic Relatedness. American Journal of Human Genetics, 98(1), 127-148. Conomos M.P., Miller M., & Thornton T. (2015). Robust Inference of Population Structure for Ancestry Prediction and Correction of Stratification in the Presence of Relatedness. Genetic Epidemiology, 39(4), 276-293. Gogarten, S. M., Bhangale, T., Conomos, M. P., Laurie, C. A., McHugh, C. P., Painter, I., ... & Laurie, C. C. (2012). GWASTools: an R/Bioconductor package for quality control and analysis of Genome-Wide Association Studies. Bioinformatics, 28(24), 3329-3331. Manichaikul, A., Mychaleckyj, J.C., Rich, S.S., Daly, K., Sale, M., & Chen, W.M. (2010). Robust relationship inference in genome-wide association studies. Bioinformatics, 26(22), 2867-2873.